implement support for tuples with optional file outputs

modules/nextflow/src/main/groovy/nextflow/processor/TaskProcessor.groovy

@@ -1335,8 +1335,10 @@ class TaskProcessor {
                 value = value instanceof Path ? value.text : value?.toString()
 
             case OptionalParam:
-                if( !value && param instanceof OptionalParam && param.optional ) {
-                    final holder = [] as MissingParam; holder.missing = param
+                def parentParam = config.outputs[param.index]
+                if( value == null && parentParam instanceof OptionalParam && parentParam.optional ) {
+                    final holder = [] as MissingParam
+                    holder.missing = param
                     tuples[param.index] = holder
                     break
                 }
@@ -1524,7 +1526,13 @@ class TaskProcessor {
             }
         }
 
-        task.setOutput( param, allFiles.size()==1 ? allFiles[0] : allFiles )
+        if( param.optional && allFiles.size() == 0 ) {
+            task.setOutput( param, null )
+        } else if( allFiles.size() == 1 ) {
+            task.setOutput( param, allFiles[0] )
+        } else {
+            task.setOutput( param, allFiles )
+        }
 
     }
 

modules/nextflow/src/main/groovy/nextflow/script/params/OptionalParam.groovy

@@ -25,7 +25,7 @@ package nextflow.script.params
  */
 trait OptionalParam {
 
-    boolean optional
+    boolean optional = false
 
     boolean getOptional() { optional }
 

modules/nextflow/src/main/groovy/nextflow/script/params/TupleOutParam.groovy

@@ -100,8 +100,10 @@ class TupleOutParam extends BaseOutParam implements OptionalParam {
     @Override
     void lazyInit() {
         super.lazyInit()
-        inner.each { opt ->
-            if( opt instanceof FileOutParam ) opt.optional(this.optional)
+        if ( this.optional ) {
+            inner.each { opt ->
+                if( opt instanceof FileOutParam ) opt.optional(this.optional)
+            }
         }
     }
 

modules/nextflow/src/test/groovy/nextflow/script/params/ParamsOutTest.groovy

@@ -1207,8 +1207,43 @@ class ParamsOutTest extends Specification {
         when:
         def process = parseAndReturnProcess(text, [:])
         TupleOutParam out0 = process.config.getOutputs().get(0)
+        out0.lazyInit()
         then:
         out0.inner[0] instanceof FileOutParam
+        out0.inner[1] instanceof FileOutParam
+        and:
+        (out0.inner[0] as FileOutParam).getName() == 'x'
+        (out0.inner[0] as FileOutParam).getMaxDepth() == 1
+        (out0.inner[0] as FileOutParam).getOptional() == false
+        and:
+        (out0.inner[1] as FileOutParam).getName() == 'y'
+        (out0.inner[1] as FileOutParam).getMaxDepth() == 2
+        (out0.inner[1] as FileOutParam).getOptional() == true
+    }
+
+    def 'check whether file optional value is overridden when tuple is optional' () {
+        given:
+        def text = '''
+            process foo {
+              output:
+              tuple path(x,maxDepth:1,optional:false), path(y,maxDepth:2,optional:true) optional false
+              tuple path(x,maxDepth:2,optional:false), path(y,maxDepth:1,optional:true) optional true
+
+              return ''
+            }
+            '''
+
+        when:
+        def process = parseAndReturnProcess(text, [:])
+        TupleOutParam out0 = process.config.getOutputs().get(0)
+        TupleOutParam out1 = process.config.getOutputs().get(1)
+        out0.lazyInit()
+        out1.lazyInit()
+        then:
+        out0.inner[0] instanceof FileOutParam
+        out0.inner[1] instanceof FileOutParam
+        out1.inner[0] instanceof FileOutParam
+        out1.inner[1] instanceof FileOutParam
         and:
         (out0.inner[0] as FileOutParam).getName() == 'x'
         (out0.inner[0] as FileOutParam).getMaxDepth() == 1
@@ -1217,6 +1252,14 @@ class ParamsOutTest extends Specification {
         (out0.inner[1] as FileOutParam).getName() == 'y'
         (out0.inner[1] as FileOutParam).getMaxDepth() == 2
         (out0.inner[1] as FileOutParam).getOptional() == true
+        and:
+        (out1.inner[0] as FileOutParam).getName() == 'x'
+        (out1.inner[0] as FileOutParam).getMaxDepth() == 2
+        (out1.inner[0] as FileOutParam).getOptional() == true
+        and:
+        (out1.inner[1] as FileOutParam).getName() == 'y'
+        (out1.inner[1] as FileOutParam).getMaxDepth() == 1
+        (out1.inner[1] as FileOutParam).getOptional() == true
     }